The issue you specifically are having on happens on files whose minimap-height is greater than that of the available minimap area, so it’s not all files, but yes, a good number. (For me, if a file goes over about 500 lines.)
But on to your suggestion of making it behave sensibly, the problem is that there’s no ‘sensible’ that works for everyone. For some people, your method whereby a single click works as expected will actually behaving erratically because they’re click-draggers. As soon as you start dragging (using your ‘sensible’ option) the mouse will be in the wrong place thus the editor will jump around. The only solution to that is to use the SetCursorPos Win32 API as MikeC suggested, but as he said it’s going to have to be built into the ST2 core. Also it may not be cross-platform compatible: I know Win32 has the function, but maybe other OSes don’t allow applications to change the cursor position programmatically. While it seems crazy for an OS not to allow applications to do this, you can see how they may wish to lock this down - it creates a bad user experience if the cursor is not where you last left it! And anyway, even if this was possible, some may still call it broken (or not ‘sensible’) due to this exact user experience breaking: “I click the minimap and it moves my mouse around. What’s that all about?”
But having said that, as MikeC said you have a lot of people with you thinking the exact same thing. The bigger issue is how to fix it without making the situation worse or just as bad.